D-I-TASSER Q9UHP6-D1

D-I-TASSER results for Q9UHP6-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q9UHP6 (107 residues)
MAHSQNSLELPININATQITTAYGHRALPKLKEELQSEDLQTRQKALMALCDLMHDPECI
YKAMNIGCMENLKALLKDSNSMVRIKTTEVLHITASHSVGRYAFLEH

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAHSQNSLELPININATQITTAYGHRALPKLKEELQSEDLQTRQKALMALCDLMHDPECIYKAMNIGCMENLKALLKDSNSMVRIKTTEVLHITASHSVGRYAFLEH
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	99876566689999941323332322447999997187268999999999999827799999998603699999982899589999999999999637889999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAHSQNSLELPININATQITTAYGHRALPKLKEELQSEDLQTRQKALMALCDLMHDPECIYKAMNIGCMENLKALLKDSNSMVRIKTTEVLHITASHSVGRYAFLEH
Prediction	85455254422561545403311343114303641647723432400320142044253024115351154035005475440243003002101434312531278
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
MAHSQNSLELPININATQITTAYGHRALPKLKEELQSEDLQTRQKALMALCDLMHDPECIYKAMNIGCMENLKALLKDSNSMVRIKTTEVLHITASHSVGRYAFLEH

4k6jA

0.12

4.28

1.50

DEthreader

ENTGHLAMELSSKAGDWFKEELRLLGGLDHIVDKVKECSLWGAERCLRVLESVTVNPENQSYLIAYSLIVSSAKALQCLVEDCMRAIIGVLLNLTNNEWGSTKTGEQ

7anwA4

0.09

3.51

1.44

SPARKS-K

RSVAGILEHMFKHSEETCQRLVAA-GGLDAVLYWCRRTDPALLRHCALALGNCALHQAVQRRMVEKRAAEWLFPLAFSKDELLRLHACLAVAVLATNKEVEREVERS

6sa8A4

0.25

0.21

6.67

1.41

MUSTER

-------------GNEQIQAVI-DAGALPALVQLLSSPNEQILQEALWALSNIASGNEQIQAVIDAGALPALVQLLSSPNEQIQDEAEKTLLNIANSEEQQKAVYDA

6sa8A5

0.27

0.23

7.17

1.30

FFAS-3D

--------------GNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGNEQIQAVID-

1wa5B

0.14

4.77

1.33

DEthreader

-R-DEADWASYSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNEQIQAVIDN

6sa8A4

0.25

0.21

6.67

1.40

SPARKS-K

-------------GNEQIQAVIDA-GALPALVQLLSSPNEQILQEALWALSNIAGGNEQIQAVIDAGALPALVQLLSSPNEQIQDEAEKTLLNIAGSEEQQKAVYDA

4rv1A2

0.20

6.29

0.53

MapAlign

-KEAARALANIASGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIAGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIAGPTSAIKAIVDA

4rv1A2

0.20

6.30

0.41

CEthreader

QKEAARALANIASGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIAGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIAGPTSAIKAIVDA

6sa8A5

0.26

0.22

6.93

1.40

MUSTER

-------------GNEQIQAVI-DAGALPALVQLLSSPNEQILQEALWALSNIASGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGNEQIQAVIDA

3tt9A2

0.18

0.16

5.15

0.84

HHsearch

-------------DNDNKLEVA-ELNGVPRLLQVLKQTDLETKKQITGLLWNLSSNDKLKNLMITEA-LLTLTENIGLLDFDIFYNVTGCLRNMSSAADGRKAMRRC

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7794

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4rv1A	0.91	1.57	0.196	0.991	model1_4rv1A.pdb.gz
2	4hxtA	0.90	1.80	0.206	1.000	model1_4hxtA.pdb.gz
3	4db6A	0.90	1.55	0.234	0.981	model1_4db6A.pdb.gz
4	6sa8A	0.90	1.54	0.234	0.981	model1_6sa8A.pdb.gz
5	4plqA	0.90	1.65	0.224	0.991	model1_4plqA.pdb.gz
6	4d49A	0.90	1.58	0.187	0.981	model1_4d49A.pdb.gz
7	1wa5B	0.89	1.76	0.140	1.000	model1_1wa5B.pdb.gz
8	4rxhB	0.89	1.73	0.121	0.991	model1_4rxhB.pdb.gz
9	5xjgA	0.88	1.68	0.132	0.981	model1_5xjgA.pdb.gz
10	3l6xA	0.88	1.85	0.168	0.991	model1_3l6xA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0022892	0.55	substrate-specific transporter activity
GO:0005048	0.54	signal sequence binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.96	single-organism process
GO:0051179	0.88	localization
GO:0051234	0.87	establishment of localization
GO:0009987	0.87	cellular process
GO:0006810	0.86	transport
GO:0051641	0.85	cellular localization
GO:0008104	0.85	protein localization
GO:0046907	0.83	intracellular transport
GO:0071702	0.82	organic substance transport
GO:0045184	0.82	establishment of protein localization
GO:0034613	0.81	cellular protein localization
GO:0015031	0.81	protein transport
GO:0044765	0.80	single-organism transport
GO:0006886	0.80	intracellular protein transport
GO:1902580	0.79	single-organism cellular localization
GO:0072594	0.79	establishment of protein localization to organelle
GO:0033365	0.79	protein localization to organelle
GO:1902593	0.78	single-organism nuclear import
GO:0034504	0.78	protein localization to nucleus
GO:0017038	0.78	protein import
GO:0016043	0.73	cellular component organization
GO:0044763	0.68	single-organism cellular process
GO:0022607	0.68	cellular component assembly
GO:0065007	0.66	biological regulation
GO:0050789	0.65	regulation of biological process
GO:0050794	0.63	regulation of cellular process
GO:0006607	0.60	NLS-bearing protein import into nucleus
GO:0032502	0.58	developmental process
GO:0044767	0.57	single-organism developmental process
GO:0048856	0.54	anatomical structure development
GO:0050896	0.53	response to stimulus
GO:0009653	0.53	anatomical structure morphogenesis
GO:0048518	0.52	positive regulation of biological process
GO:0045216	0.52	cell-cell junction organization
GO:0032501	0.52	multicellular organismal process
GO:0022610	0.52	biological adhesion
GO:0051716	0.51	cellular response to stimulus
GO:0048513	0.51	animal organ development
GO:0044707	0.51	single-multicellular organism process
GO:0034329	0.51	cell junction assembly
GO:0048522	0.50	positive regulation of cellular process
GO:0007389	0.50	pattern specification process
GO:0002009	0.50	morphogenesis of an epithelium

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0005737	0.97	cytoplasm
GO:0043229	0.95	intracellular organelle
GO:0043231	0.94	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0044422	0.87	organelle part
GO:0044446	0.86	intracellular organelle part
GO:0044444	0.86	cytoplasmic part
GO:0044428	0.75	nuclear part
GO:0016020	0.71	membrane
GO:0005829	0.71	cytosol
GO:0005654	0.56	nucleoplasm
GO:0005643	0.51	nuclear pore

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1lf6A	0.626	3.44	0.020	0.944	3.2.1.3	NA
2	0.060	1ho8A	0.736	2.54	0.058	0.925	3.6.3.14	72
3	0.060	1js4A	0.564	3.40	0.075	0.822	3.2.1.4	NA
4	0.060	1gaiA	0.567	3.92	0.030	0.925	3.2.1.3	NA
5	0.060	1z1wA	0.600	3.33	0.073	0.869	3.4.11.-	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.11	1bk6A	0.895	1.70	0.140	0.991	0.60	III	complex1.pdb.gz	48,52,55,56,86,89,93,97
2	0.09	3l3qA	0.872	1.83	0.103	0.991	0.58	III	complex2.pdb.gz	13,15,19,53,54,60,89
3	0.07	1q1tC	0.874	1.77	0.140	0.991	0.52	III	complex3.pdb.gz	12,13,15,19,48,52,53,54,55,60,88
4	0.07	2gl7D	0.840	1.96	0.142	0.981	0.56	III	complex4.pdb.gz	63,66,69,98
5	0.04	1i7x0	0.838	1.95	0.142	0.981	1.01	III	complex5.pdb.gz	33,64,65,66,67,70,98,99,102,103,105
6	0.04	2jdq0	0.881	1.72	0.112	0.991	1.07	III	complex6.pdb.gz	29,32,33,36,61,64,65,66,67,70,99,100,106
7	0.04	1y2aC	0.883	1.88	0.142	0.981	0.52	III	complex7.pdb.gz	19,45,48,52,56,89,93,96
8	0.04	3obvA	0.780	2.33	0.152	0.972	0.57	SUC	complex8.pdb.gz	66,69,73,100
9	0.03	3obvB	0.787	2.30	0.143	0.972	0.57	SUC	complex9.pdb.gz	32,59,60,63,64,67

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.